Contacts of the strand formed by residues 73 - 80 (chain A) in PDB entry 1MPX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ALA* 4.5 9.2 - - + -
71A LYS 4.0 7.0 - - - +
72A ASN* 1.3 77.1 - - - +
74A PRO* 1.3 70.6 - - + +
111A GLY 3.6 19.1 - - - +
113A ILE* 3.8 21.0 - - + +
163A GLU 3.0 6.2 + - - +
164A SER* 3.0 27.7 + - - -
165A ASN* 3.2 3.3 + - - -
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Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN 4.2 3.4 - - - +
73A ALA* 1.3 90.4 - - + +
75A ILE* 1.3 60.2 + - - +
110A GLY 5.5 1.8 - - - +
111A GLY 4.7 5.4 - - - +
112A TYR* 3.3 30.4 - - + -
113A ILE* 3.0 25.5 + - - +
165A ASN* 3.4 14.8 - - - +
167A LYS 3.7 2.2 - - - +
376A LEU* 3.5 36.3 - - + +
377A VAL* 4.0 17.5 - - + -
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PRO* 1.3 75.6 - - - +
76A VAL* 1.3 71.8 + - - +
77A LEU* 4.2 4.7 - - + +
113A ILE* 3.3 22.2 - - + -
115A VAL* 3.7 24.2 - - + -
157A LEU* 4.3 34.5 - - + +
158A VAL* 5.2 1.1 - - + +
161A VAL* 4.5 9.0 - - + -
164A SER* 3.2 31.4 - - - +
167A LYS 3.1 11.7 + - - +
168A VAL* 3.4 21.0 - - + -
169A GLY* 2.9 24.6 + - - -
376A LEU* 4.4 3.5 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 1.3 75.0 - - - +
77A LEU* 1.3 59.0 + - - +
107A PHE* 3.8 17.7 - - + -
112A TYR* 3.3 32.5 - - + -
113A ILE 3.0 7.6 + - - +
114A ARG* 3.2 28.1 + - - +
115A VAL 2.9 24.4 + - - -
169A GLY 3.3 3.8 - - - +
171A ILE* 3.5 32.8 - - + -
372A PHE* 3.7 23.3 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 4.0 5.8 - - + -
76A VAL* 1.3 72.8 - - - +
78A THR* 1.3 77.9 + - - +
79A ARG* 4.4 13.2 - - + -
114A ARG* 4.4 0.2 + - - -
115A VAL* 3.4 28.9 - - + +
117A GLN* 4.6 4.3 - - + -
150A ALA 5.1 0.4 - - - +
153A THR* 4.0 21.8 - - + -
154A ILE* 3.8 30.1 - - + -
157A LEU* 4.3 8.3 - - + -
168A VAL* 4.1 9.2 - - + -
169A GLY 2.8 14.1 + - - +
170A MSE 3.3 24.7 - - + +
171A ILE 3.2 24.4 + - - -
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 1.3 73.8 + - - +
79A ARG* 1.3 65.8 + - - +
80A THR 4.1 0.4 + - - -
114A ARG* 3.0 28.9 + - - -
115A VAL 2.9 5.3 + - - +
116A PHE* 3.3 21.9 - - + -
117A GLN 2.9 24.9 + - - -
170A MSE 5.4 1.1 - - - -
171A ILE* 2.6 25.7 + - - +
172A GLY* 4.4 1.0 - - - -
176A GLU* 3.5 39.9 - - + +
180A VAL* 6.2 0.2 - - - -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.4 12.1 - - - +
77A LEU* 4.4 13.9 - - + -
78A THR* 1.3 77.0 - - - +
80A THR* 1.3 60.7 + - - +
117A GLN* 2.9 35.1 + - + +
119A VAL* 4.0 18.7 - - + +
146A HIS* 3.2 37.4 + - - +
149A ASP* 3.4 28.6 + - - +
150A ALA* 3.8 28.9 - - - +
153A THR* 4.4 0.6 + - - -
170A MSE 3.9 20.3 - - + +
175A TYR 4.4 0.2 - - - +
176A GLU* 3.7 9.9 - - - -
179A THR* 2.8 42.6 + - + +
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR* 4.6 2.0 - - - -
79A ARG* 1.3 74.6 - - - +
81A PRO* 1.3 66.8 - - - +
82A TYR* 2.9 20.9 + - - +
83A ASP 4.3 2.0 - - - +
84A ALA* 4.0 27.4 - - - +
87A ARG* 4.4 1.8 - - + -
116A PHE* 4.2 12.6 - - + -
117A GLN 2.8 18.0 + - - +
118A ASP* 3.4 4.7 - - - +
119A VAL* 3.0 26.3 + - - +
176A GLU* 2.5 33.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il